Method of obtaining a peptide with desired target property

ABSTRACT

A method to obtain selected individual peptides or families thereof which have a target property and optionally to determine the amino acid sequence of a selected peptide or peptides to permit synthesis in practical quantities is disclosed. In general outline, the method of the invention comprises synthesizing a mixture of randomly or deliberately generated peptides using standard synthesis techniques, but adjusting the individual concentrations of the components of a mixture of sequentially added amino acids according to the coupling constants for each amino acid/amino acid coupling. The subgroup of peptides having the target property can then be selected, and either each peptide isolated and sequenced, or analysis performed on the mixture to permit its composition to be reproduced. Also included in the invention is an efficient method to determine the relevant coupling constants.

CROSS REFERENCE

This application is a continuation of an earlier filed pending U.S.application Ser. No. 07/525,899 filed May 18, 1990 (now issued U.S. Pat.No. 5,266,684 issued Nov. 30, 1993) which application is a divisional ofU.S. application Ser. No. 07/189,318 filed May 2, 1988, which issued asU.S. Pat. No. 5,010,175 on Apr. 23, 1991, which applications areincorporated herein by reference in their entirety and to whichapplications we claim priority under 35 USC S120.

TECHNICAL FIELD

The invention relates to synthesis identification, and analysis methodsto obtain desired peptide sequences. More particularly, it concerns amethod to obtain defined peptide mixtures, to select those which havehigh affinities for receptor (or other desired property) and to identifyand analyze desired members of these mixtures.

BACKGROUND ART

It is now almost a matter of routine to synthesize a single definedpeptide sequence using the Merrifield method to "grow" peptide chainsattached to solid supports. The process of synthesizing these individualpeptides has, in fact, been automated, and commercially availableequipment can be used to synthesize routinely peptides of twenty or moreamino acids in length. To obtain peptides of arbitrary length, theresulting peptides can further be ligated with each other by usingappropriate protective groups on the side chains and by employingtechniques permitting the removal of the synthesized peptides from thesolid supports without deprotecting them. Thus, the synthesis ofindividual peptides of arbitrary length is known in the art.

However routine the synthesis of individual peptides may be, it isnecessarily laborious. Therefore, in the many cases where it is notpreviously known which of a multiplicity of peptides is, in fact, thepreparation desired, while theoretically it is possible to synthesizeall possible candidates and test them with whatever assay is relevant(immunoreactivity with a specific antibody, interaction with a specificreceptor, particular biological activity, etc.), to do so using theforegoing method would be comparable to the generation of the proverbialShakespeare play by the infinite number of monkeys with their infinitenumber of typewriters. In general, the search for suitable peptides fora particular purpose has been conducted only in cases where there issome prior knowledge of the most probable successful sequence.Therefore, methods to systematize the synthesis of a multiplicity ofpeptides for testing in assay systems would have great benefits inefficiency and economy, and permit extrapolation to cases where nothingis known about the desired sequence.

Two such methods have so far been disclosed. One of them, that ofHoughten, R. A., Proc Natl Acad Sci USA (1985) 82:5131-5135, is amodification of the above Merrifield method using individualpolyethylene bags. In the general Merrifield method, the C-terminalamino acid of the desired peptide is attached to a solid support, andthe peptide chain is formed by sequentially adding amino acid residues,thus extending the chain to the N-terminus. The additions are carriedout in sequential steps involving deprotection, attachment of the nextamino acid residue in protected form, deprotection of the peptide,attachment of the next protected residue, and so forth.

In the Houghten method, individual polyethylene bags containingC-terminal amino acids bound to solid support can be mixed and matchedthrough the sequential attachment procedures so that, for example,twenty bags containing different C-terminal residues attached to thesupport can be simultaneously deprotected and treated with the sameprotected amino acid residue to be next attached, and then recovered andtreated uniformly or differently, as desired. The resultant of this is aseries of polyethylene bags each containing a different peptidesequence. These sequences can then be recovered and individuallybiologically tested.

An alternative method has been devised by Geysen, H. M., et al, ProcNatl Acad Sci USA (1984) 81:3998-4002. See also WO86/06487 andWO86/00991. This method is a modification of the Merrifield systemwherein the C-terminal amino acid residues are bound to solid supportsin the form of polyethylene pins and the pins treated individually orcollectively in sequence to attach the remaining amino acid residues.Without removing the peptides from support, these peptides can thenefficiently be effectively individually assessed for the desiredactivity, in the case of the Geysen work, interaction with a givenantibody. The Geysen procedure results in considerable gains inefficiency of both the synthesis and testing procedures, whilenevertheless producing individual different peptides. It is workable,however, only in instances where the assay can be practically conductedon the pin-type supports used. If solution assay methods are required,the Geysen approach would be impractical.

Thus, there remains a need for an efficient method to synthesize amultiplicity of peptides and to select and analyze these peptides forthose which have a particular desired biological property. The presentinvention offers such an alternative by utilizing synthesis of mixturesas well as providing a means to isolate and analyze those members orfamilies of members of the mixture which have the desired property.

DISCLOSURE OF THE INVENTION

By adjustment of the appropriate parameters, the invention permits, forthe first time, a practical synthesis of a mixture of a multitude ofpeptide sequences, in predictable or defined amounts within acceptablevariation, for the intended purpose. In addition, the invention permitsthis mixture to be selected for the desired peptide members,individually or as groups and the determination of sequences of theseselected peptides so that they can be synthesized in large amounts ifdesired. Because mixtures of many peptides are used, prejudicialassumptions about the nature of the sequences required for the targetbiological activity is circumvented.

Thus, in one aspect, the invention is directed to a method to synthesizea mixture of peptides of defined composition. The relative amount ofeach peptide in the mixture is controlled by modifying the generalMerrifield approach using mixtures of activated amino acids at eachsequential attachment step, and, if desired, mixtures of starting resinswith C-terminal amino acids or peptides conjugated to them. Thecompositions of these mixtures are controlled according to the desireddefined composition to be obtained by adjustment of individual activatedamino acid concentrations according to the rate constants determined forcoupling in the particular ligation reactions involved. The inventionalso provides, and is directed to, a method to determine efficiently therequired rate constants appropriate to the specific conditions underwhich the reaction will be conducted.

It should be noted that while the invention method of synthesis is mostusually and practically conducted using solid-supported peptides, thereis no reason it cannot be employed for solution phase synthesis, whereinthe acceptor amino acid or peptide is simply blocked at the carboxylterminus.

In another aspect, the invention is directed to a method to select thosecomponents (individually or as families) of the mixture which have thedesired "target" activity. Sequence information on these peptides canalso be obtained. Thus, the invention is also directed to a method toseparate the desired peptide, or peptide family, from the originalcomposition; this comprises effecting differential behavior underconditions which result in physical separation of components, such asbinding to a selective moiety, differential behavior with respect tosolubility, shape or transport, or modification of the structure ofselected peptides or mixtures by a reagent or enzyme which converts onlythe desired peptides to a form that can be conveniently analyzed orseparated.

Finally, the invention is directed to the combination of the foregoingwith methods to analyze peptide sequences, often while these sequencesare still present in mixtures.

In addition to the foregoing aspects, various additional combinationsthereof are useful.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a table showing the results of analysis of dipeptides formedusing mixtures of activated amino acids with various acceptors.

FIG. 2 is a graphical representation of relative rates of conjugation ofactivated amino acids to solid support-linked peptides with variousN-terminal amino acids as tabulated in FIG. 1.

FIG. 3 shows the results of concentration controlled synthesis of aminoacid mixtures.

FIGS. 4A and 4B show HPLC traces in one and two dimensions respectivelyof a peptide mixture.

FIG. 5 shows a graph of absorbance areas obtained from HPLC of apentapeptide mixture.

FIG. 6 is a table showing the results of HPLC separation of a modelpentapeptide mixture.

FIG. 7 is a table showing the results of sequencing performed on apentapeptide mixture.

MODES OF CARRYING OUT THE INVENTION

In general, the goal of the invention is to provide a means to obtainand identify one or a family of specific peptide sequences which have atarget utility such as ability to bind a specific receptor or enzyme,immunoreactivity with a particular antibody, and so forth. To achievethis end, the method of the invention involves one or more of the threefollowing steps:

1. Preparation of a mixture of many peptides putatively containing thedesired sequences;

2. Retrieval or selection from the mixture of the subpopulation whichhas the desired characteristics; and

3. Analysis of the selected subpopulation to determine amino acidsequence so that the desired peptide(s) can be synthesized alone and inquantity.

Of course, repeated iterations of the three steps using smaller andsmaller populations can also be conducted.

Since a complex mixture of peptides is to be synthesized as the startingmaterial for selection, no preconceived ideas of what the nature of thepeptide sequence might be is required. This is not to imply that themethod is inapplicable when preliminary assumptions can reasonably bemade. In fact, the ability to make valid assumptions about the nature ofthe desired sequence makes the conduct of the method easier.

Using for illustration only the twenty amino acids encoded by genes, amixture in which each position of the peptide is independently one ofthese amino acids will contain 400 members if the peptide is adipeptide; 8,000 members if it is a tripepride; 160,000, if it is atetrapeptide; 3,200,000 if there are five amino acids in the sequence;and 64,000,000 if there are six. Since alternative forms can beincluded, such as D amino acids, and noncoded amino acids, the number ofpossibilities is, in fact, dramatically greater. The mixtures, in orderto be subjected to procedures for selection and analysis of the desiredmembers, must provide enough of each member to permit this selection andanalysis. Using the current requirement, imposed by limitations ofavailable selection and analysis techniques, of about 100 picomoles of apeptide in order to select it and analyze its structure, the totalamount of protein mixture required can be calculated, assuming that thepeptides are present in equal amounts. The results of this calculationfor peptides containing amino acids selected only from those encoded bythe gene are shown in Table 1 below.

It is essential that the synthesis of the mixture be controlled so thecomponent peptides are present in approximately equal, or at leastpredictable, amounts. If this is achieved, then quantitation of thepeptides selected by a protein receptor, or other method, will reflectthe dissociation constants of the protein-peptide complexes. If thecomponents of the mixture differ greatly, the amount of selected peptidewill also reflect the concentration of that peptide in the mixture.Since it will not be feasible to quantitate the individual amounts ofthe components of very large mixtures of peptides, it is imperative thatthe synthesis is predictably controlled.

                  TABLE 1                                                         ______________________________________                                        n          Number of Peptides                                                                          Mass of Mixture                                      ______________________________________                                        2          400           0.0022    mg                                         3          8,000         0.44      mg                                         4          160,000       8.8       mg                                         5          3,200,000     176       mg                                         6          64,000,000    3.5       g                                          ______________________________________                                    

As shown in the table, even for a peptide of 6 amino acids wherein themixture contains 64,000,000 separate components, only about 3.5 g oftotal mixture is required. Since most epitopes for immunoreactivity areoften no greater than this length, and receptor binding sites areregions of peptides which may be of similar length, it would befeasible, even at current levels of sensitivity in selection andanalysis, to provide a complete random mixture of candidate peptides,without presupposition or "second guessing" the desired sequence. Thisis further aided if peptides with staggered regions of variable residuesand residues common to all components of the mixture can be used, asoutlined below.

While the most frequent application of the invention is to discern anindividual or small subgroup of amino acid sequences having a desiredactivity, in some instances it may be desirable simply to provide themixture per se. Instances in which this type of mixture is usefulinclude those wherein several peptides may have a cooperative effect,and in the construction of affinity columns for purification of severalcomponents. The method may also be used to provide a mixture of alimited number of peptides, which can then be separated into theindividual components, offering a method of synthesis of large numbersof individual peptides which is more efficient than that provided byindividual synthesis of these peptides.

As used herein, the "acceptor" is the N-terminal amino acid of asolid-supported growing peptide or of the peptide or amino acid insolution which is protected at the C-terminus; the "activated" aminoacid is the residue to be added at this N-terminus. "Activated" isapplied to the status of the carboxyl group of this amino acid ascompared to its amino group. The "activated" amino acid is suppliedunder conditions wherein the carboxyl but not the amino group isavailable for peptide bond formation. For example, the carboxyl need notbe derivatized if the amino group is blocked.

"Target" characteristic or property refers to that desired to beexhibited by the peptide or family, such as specific bindingcharacteristics, contractile activity, behavior as a substrate, activityas a gene regulator, etc.

A. Synthesis of Mixtures of Defined Composition

Two general approaches to the synthesis of defined mixtures aredisclosed. The first approach results in a completely arbitrary mixtureof all possible peptides containing "n" amino acid residues inapproximately equal or predictable amounts, and requires for success thedetermination of all of the relative rate constants for couplingsinvolved in constructing the desired peptides in the mixture. The secondapproach takes advantage of certain approximations, but requires thatcompromises be made with regard to the sequences obtained.

The discussion below in regard to both approaches will concern itselfwith synthesis of peptides containing residues of the twenty amino acidsencoded by the genetic code. This is for convenience in discussion, andthe invention is not thus limited. Alternate amino acid residues, suchas hydroxyproline, α-aminoisobutyric acid, sarcosine, citrulline,cysteic acid, t-butylglycine, t-butylalanine, phenylglycine,cyclohexylalanine, β-alanine, 4-aminobutyric acid, and so forth can alsobe included in the peptide sequence in a completely analogous way. The Dforms of the encoded amino acids and of alternate amino acids can, ofcourse, also be employed. The manner of determining relative rateconstants, of conducting syntheses, and of conducting selection andanalysis is entirely analogous to that described below for the naturallyoccurring amino acids. Accordingly, the results in terms of the numberof rate constants required, the number of representative peptides in themixture, etc., are also directly applicable to peptides which include asone, or more, or all residues, these nonencoded amino acids.

As a general proposition, it is not so simple to obtain mixtures ofpeptides having a defined composition, as might be supposed. Using thegeneral Merrifield approach, one might assume that a mixture of twentydifferent derivatized resins, each derivatized with a different aminoacid encoded by the gene, might be simultaneously reacted with a mixturecontaining the N-blocked, activated esters of the twenty amino acids.The random reaction of the activated amino acids with the derivatizedresins would then, presumably, result in the 400 possible dipeptidecombinations.

But this would only be the result if the rate of all 400 possiblecouplings were the same. A moment's reflection will serve to indicatethat this is not likely to be the case. The rate of coupling of thesuitably N-blocked activated carboxyl form of alanine with a resinderivatized with alanine is, indeed, not the same as the rate ofreaction of N-blocked carboxy-activated proline with a resin derivatizedwith alanine, which is, in turn, not the same as the rate of reaction ofthe N-blocked carboxy-activated proline with a resin derivatized withproline. Each of the 400 possible amino acid couplings will have its owncharacteristic rate constant. In order to prevent the mixture fromcontaining an undue preponderance of the dipeptides formed in reactionshaving the faster rate constants, adjustments must be made. The problemwill be aggravated upon the attempt to extend the peptide chain with thethird mixture of twenty amino acids, and further complicated byextension with the fourth, etc. As more amino acids are added to thechain, the preference for the higher coupling constants is continuouslytilted in favor of the faster reacting species to the near exclusion ofthe peptides which would result from the slower coupling constants.

According to the method of the invention, the differential in couplingconstants is compensated by adjustment of the concentrations of thereactants. Reactants which participate in reactions having couplingconstants which are relatively slow are provided in higher concentrationthan those which participate in reactions having coupling constantswhich are fast. The relative amounts can be precisely calculated basedon the known or determined relative rate constants for the individualcouplings so that, for example, an equimolar mixture of the peptidesresults, or so that a mixture having an unequal, but definedconcentration of the various peptides results.

The method is similarly applied to solution phase synthesis, wherein theacceptor peptides or amino acids are supplied as a mixture for reactionwith an appropriate mixture of activated amino acids. Either or bothmixtures are concentration-adjusted to account for rate constantdifferentials.

A.1 Determination of Coupling Constants

In order to adjust the relative concentrations of reactants, it is, ofcourse, necessary to know the relative rate constants on the basis ofwhich adjustment will be made. The invention method offers a directmeans to obtain sufficiently precise values for these relative rateconstants, specifically in the context of the reaction conditions thatwill be used for the peptide mixture synthesis.

Alternative methods available in the art for estimating the 400 rateconstants needed for synthesis of peptides utilizing all twenty"natural" amino acids are based on hypothesis and extrapolation. Forexample, Kemp, D. S. et al, J Org Chem (1974) 39:3841-3843, suggested acalculation based on the coupling Go glycine of the nineteen remainingamino acids and of glycine to the remaining nineteen, and then relatingthese to the constant for Gly-Gly coupling. This method, indeed,predicted that certain couplings would have aberrant rate constants, inparticular those wherein the N-unblocked acceptor amino acid was aprolyl residue.

In addition, Kovacs, J., in "The Peptides: Analysis, Synthesis, Biology"(1980), Gross, et al, ed, pp 485-539 provided a method to extrapolaterate constants for studied couplings to those not studied based on thenature of the side chains, solvents and other conditions. Thesepredicted values in general agreed with those of Kemp.

The method of the present invention, however, provides for a precisedetermination of any desired coupling constant relative to the othersunder the specific conditions intended to be used in the synthesis. Itis applicable not only to the twenty "natural" amino acids studied byothers, but to D-forms and non-coded amino acids as well. The methodemploys, for example, the polypropylene-bagged resins of Houghten, R.(supra). Each of the twenty amino acyl resins is packaged in apolypropylene bag, and the twenty packets are placed in one containerhaving excess amounts of all twenty activated amino acids. Reaction isallowed to proceed for a set period sufficient to complete coupling tothe acceptor amino acids linked to resin. Each of the bags is thensubjected to treatment to release the dipeptides, resulting in twentymixtures of twenty dipeptides each, each mixture being analyzedseparately, using standard techniques of amino acid analysis. Therelative amounts of the N-terminal amino acids for the mixture of eachparticular bag represents the relative values of the coupling constantsof each of these amino acids for the same C-terminal residue. Therelative amount of coupling between various bags gives the comparativeactivities of the residues as acceptors. Thus analysis of all twentybags thus results in relative values for the 400 desired constants. Thecouplings can be conducted in a manner and under conditions preciselythe same as those expected to be used for the synthesis; the nature ofactivating, blocking, and protecting groups can also be standardized.

(If absolute rate constants are desired, absolute values can bedetermined for a given activated amino acid with respect to eachacceptor and the remainder calculated from the appropriate ratios.)

A.2 Adjustment of Concentrations

The relative rate constants determined as described above can then beused in adjusting the concentrations of components in synthesizing thedesired mixture of defined concentration. In principle, theconcentrations of the components which are slowly reactive areincreased, and the expected resulting concentration of products iscalculated. In order to obtain a mixture of equimolar concentration, thevarious rate constants must be accounted for in an algorithm which isnot straightforward to calculate, since the effect of concentration ofthe activated participant in the coupling will be different depending onthe acceptor component, and conversely. Computer-based simulationsinvolving all parameters can be designed.

In practice, a mixture of acceptors on a resin with similar relativereactivities is reacted with the appropriate mixture of knownconcentrations of activated amino acids. The identity and quantity ofproducts are determined from known values (amount of reactants used, andamounts of products formed), the relative rate constants for each of thecouplings are calculated. Knowing the relative rate constants and therelative amounts of products desired, the amounts of reactants can beadjusted to achieve this goal. Currently, the computations are performedby the Euler or second-order Runge-Kutta methods (see Press, W. et al,"Numerical Recipes" (1986) Cambridge University Press, New York, chapter15).

However, this is usually not needed. Under ordinary application of themethod, the acceptor concentration is held constant for all acceptors ofsimilar reactivity, and only the activated residue concentration isvaried inversely as to its relative rate of coupling. Acceptors whichdiffer in their capacity to couple are used in separate reactionmixtures, as outlined below.

The remainder of the synthesis method employs known procedures. Acoupling protocol is designed wherein the initial mixture of allderivatized resins is similarly reactive compared to the others with theactivated, protected next amino acid residue or mixture. After thisinitial coupling, unreacted amino groups can, if needed, be capped, forexample with acetyl groups, by reacting with acetic anhydride, thereacted amino acyl residues are deblocked, and next N-blocked,C-activated amino acid residue mixture added. After this addition step,the unreacted amino groups can, if desired, again be capped, and thereacted residues deprotected and treated with the subsequent N-blocked,C-activated amino acid.

Isolation of full-length peptides can be further aided by utilizing afinal amino acyl residue which is blocked with a selectable group suchas tBOC-biotin. When the side chains are deprotected and peptidereleased from the resin, only full-length peptides will have biotin atthe amino terminus, which facilitates their separation from the cappedpeptides. The biotinylated peptides (which are all full length due tothe intermediate capping of incomplete peptides) are convenientlyseparated from the capped peptides by avidin affinity chromatography.Other specific selectable groups can be used in connection with theprotecting group on the final amino acid residue to aid in separation,such as, for example, FMOC, which can also be removed.

In the above-described approach, in order to vary the ratios only ofactivated residues in a particular mixture, it has been assumed that allacceptors have the same relative rates with all activated amino acids.If they do not [for example Pro has been reported to differ in relativerate from other acceptors (Kemp, D. S. et al, J Org Chem (1974)39:3841-3843 (supra))], the simple approach thus far described will becompromised since one cannot conveniently adjust the relativeconcentrations of the acceptors once coupled to the solid phase. Thiscan be resolved if the acceptors are first separated into groups whichhave similar relative rates of reactivities. It may also be advantageousfor technical reasons, in some cases, to separate acceptors into groupsbased on their relative rates of reaction, for example, the separationof the very "fast" from the very "slow" reacting acceptors. The ensuingdescription utilizes "slow" and "fast" to differentiate acceptors whichdiffer in relative rates of coupling with activated amino acids.

In this method, the reaction rates can be normalized to some extent byconducting "slow" and "fast" reactions separately and then sorting intoalternate sets to reverse the reactivity rates. This general approach isillustrated as follows. ##STR1##

As shown above, resins bearing amino acid residues which "slowly"conjugate as acceptors for additional residues are reacted separatelyfrom those bearing acceptors which have "fast" relative couplingconstants. Depending on the particular amino acid from the mixture whichsubsequently couples, the growing chain will bear, as the N-terminus, anacceptor which is either a "slow" or "fast" reactor. As in every step,slow- and fast-reacting acceptors are conjugated in separate reactions;thus the resins bound to dipeptides N-terminated in slow- andfast-coupled receptors are segregated; each step involves four mixturesas shown. The resins bearing peptides N-terminated in fast couplers areagain reacted separately from those N-terminated with slow couplers alsosegregating the activated residues according to whether they will beslow or fast acceptors when added to the peptide in the second couplingreaction. The sorting is repeated after this reaction, and the fastcouplers again segregated from their slower counterparts to continue thesynthesis. In instances where the rate of coupling is determinedpredominately by the coupling constant typical of the acceptor, this"mix-and-match" technique permits ready construction of an approximatelyequimolar mixture without adjusting the ratios of acceptor in thereaction mixtures.

A.3 Modified Synthesis of Mixtures

In addition to achieving the synthesis of mixtures of randomconfiguration or any particular desired composition by regulating therelative amounts of each sequential residue to be added, a modifiedapproach can be used to obtain particular desired mixtures byintroducing acceptable limitations into the sequences of resultingpeptides.

For example, positions occupied by each of the twenty candidate aminoacids obtained by using mixtures of N-blocked, C-activated amino acidresidues in a synthesis step are alternated with positions having thesame residue common to all of the peptides in the mixture. In this way,manipulation of concentrations to account for only twenty different rateconstants is required in adding the mixture, while the addition of thesubsequent common residue can be effected by running the reaction tocompletion. For example, mixtures of the peptides of the sequence (N toC) AA₁ -Ala-AA₃ -Pro-AA₅ -Gly could be synthesized by usingGly-derivatized resin in the presence of a mixture of blocked, activatedamino acids whose concentration ratios are adjusted in inverseproportion to their rate constants for coupling to glycine. (Thereaction product can be capped, for example, with acetic anhydride, andthen the protected amino groups deblocked for subsequent reaction withan excess of N-blocked, activated proline.) When this addition reactionhas gone to completion, the resin is again capped, the protected aminogroups deblocked, and a mixture of blocked, activated amino acidsinversely proportional in their concentration to their couplingconstants with proline residues is added. Subsequent cycles employ anexcess of alanine and the appropriate mixture of amino acid residuesbased on their relative coupling constants to the alanine.

Although the foregoing method places some constraints on the complexityof the resulting mixture, it is, of course, possible to obtain as manymembers of the mixture as previously, and the algorithms for computingthe appropriate mixtures are greatly simplified.

B. Selection

Since the method of the invention results in a complex mixture ofpeptides, only a few of which are those desired for the targetreactivity, it is necessary to select from the mixture those successfulproducts which have the required properties. The nature of the selectionprocess depends, of course, on the nature of the product for whichselection is to be had. In a common instance, wherein the desiredproperty is the ability to bind a protein such as an immunoglobulin,receptor, receptor-binding ligand, antigen or enzyme, selection can beconducted simply by exposing the mixture to the substance to whichbinding is desired. The desired peptides will bind preferentially.(Other, non-protein substances, such as carbohydrates or nucleic acidscould also be used.) The bound substances are then separated from theremainder of the mixture (for example, by using the binding substanceconjugated to a solid support and separating using chromatographictechniques or by filtration or centrifugation, or separating bound andunbound peptides on the basis of size using gel filtration). The boundpeptides can then be removed by denaturation of the complex, or bycompetition with the naturally occurring substrate which normally bindsto the receptor or antibody.

This general method is also applicable to proteins responsible for generegulation as these peptides bind specifically to certain DNA sequences.

In the alternative, peptides which are substrates for enzymes such asproteases can be separated from the remainder of the peptides on thebasis of the size of cleavage products, or substrates for enzymes whichadd a selectable component can be separated accordingly.

Other properties upon which separation can be based include selectivemembrane transport, size separation based on differential behavior dueto 3-dimensional conformation (folding) and differences in otherphysical properties such as solubility or freezing point.

Since a number of the members of the mixture are expected to possess thedesired target property to a greater or lesser degree, it may benecessary to separate further the components of the smaller mixturewhich has been selected by standard differentiating chromatographictechniques such as HPLC. On the other hand, it may be desirable to usethe subgroup without further separation as a "family" to provide thedesired activity. However, in any case, if very large subpopulations areobtained, reapplication of the selection technique at higher stringencymay be needed. Analysis, as set forth below, can be conducted onindividual components, or on mixtures having limited numbers ofcomponents.

Thus, for example, if a mixture of peptides binding to antibody orreceptor contains fifty or so members, the salt concentration or pH canbe adjusted to dissociate all but the most tightly binding members, orthe natural substrate can be used to provide competition. Thisrefinement will result in the recovery of a mixture with a moremanageable number of components. A variety of protocols will be evidentto differentiate among peptides with varying levels of the targetcharacteristics.

C. Analysis

When individual peptides or manageable mixtures have been obtained,standard methods of analysis can be used to obtain the sequenceinformation needed to specify the particular peptide recovered. Thesemethods include determination of amino acid composition, including theuse of highly sensitive and automated methods such as fast atombombardment mass spectrometry (FABMS) which provides the very precisemolecular weight of the peptide components of the mixture and thuspermits the determination of precise amino acid composition. Additionalsequence information may be necessary to specify the precise sequence ofthe protein, however. In any event, current technology for sequenceanalysis permits determination on about 100 picomoles of peptide orless. A variety of analytical techniques are known in the art, anduseful in the invention, as described below:

It should be emphasized that certain of these methods can be applieddirectly to mixtures having limited numbers of components, and thesequence of each component deduced. This application is made withoutprior separation of the individual components.

The ultimate success of the method in most cases depends on sequenceanalysis and, in some cases, quantitation of the individual peptides inthe selected mixture. Techniques which are current state-of-artmethodologies can be applied individually on pure components but alsomay be used in combination as screens. A combination of diode arraydetection Liquid Chromatography (DAD-LC), mixture peptide sequencing,mass spectrometry and amino acid analysis is used. To Applicants'knowledge, these standard methods are used for the first time incombination directly on the peptide mixtures to aid in the analysis. Thefollowing paragraphs briefly describe these techniques.

HPLC with single wavelength detection provides a rapid estimation of thecomplexity of mixture and gives a very approximate estimation of amountsof components. This information is contained within the more preciseinformation obtained in DAD-LC.

DAD-LC provides complete, multiple spectra for each HPLC peak, which, bycomparison, can provide indication of peak purity. These data can alsoassign presence of Tyr, Trp, Phe, and possibly others (His, Met, Cys)and can quantitate these amino acids by 2nd derivative ormulti-component analysis. By a post-column derivatization, DAD-LC canalso identify and quantitate Cys, His and Arg in individual peptides.Thus, it is possible to analyze for 6 of the 20 amino acids of eachseparated peptide in a single LC run, and information can be obtainedabout presence or absence of these amino acids in a given peptide in asingle step. This is assisted by knowing the number of residues in eachpeptide, as is the case in application to the present invention. Also,by correction at 205 nm absorbance for side-chain chromophores, thistechnique can give much better estimation of relative amounts of eachpeptide.

Mass spectrometry identifies molecules according to mass and canidentify peptides with unique composition, but does not distinguishisomeric sequences. In effect, this method provides similar results asthe amino acid analysis (AAA) of isolated peptides; the advantage isthat it can be performed on mixtures in a single experiment. Thedisadvantage is that as applied to mixtures it does not tell whichpeptide belongs to which LC peak nor provide quantitation; further, somepeptides may go undetected. For the present purpose, it is useful inconjunction with one of the other methods.

Mixture peptide sequencing is most useful for identification, especiallyif the selected peptides are limited in number. As sequence cycles areperformed through positions where multiple amino acids were placed, thepeptides show multiple derivatized amino acids present in proportion totheir amount in the selected peptide. In many cases quantitation of theamino acids in the different cycles will resolve this potential problem;if amino acids are present in the same sequence, they should appear inidentical amounts as in the sequencing cycles. Thus, the problem issignificant when two or more selected peptides are present in similaramounts. In this case they may be readily distinguishable by combineduse of other methods mentioned. As a final resort, group separations orreactions may be performed so that sequencing will provide a uniquesolution.

HPLC separation and amino acid analysis or sequencing of componentscould also be performed. Amino acid analysis provides composition, butnot sequence. Likewise, the isolated peptides can be sequenced to givethe exact solutions of identity. Isolation is more tedious than analysisof mixes, and not doable for very large mixtures; these methods however,are quite practical for a limited number of peptides.

D. Summary

The foregoing approach of preparation of complex mixtures, selection ofthose members having successful properties, and, if desired, analysis ofthe chosen few so as to permit large-scale synthesis of the desiredpeptides permits selection of one or more peptides of a mixture whichare superior in their properties in binding to various moietiesincluding proteins, such as enzymes, receptors, receptor-binding ligandsor antibodies, nucleic acids, and carbohydrates, reaction with enzymesto form distinct products, or other properties such as transport throughmembranes, anti-freeze properties, and as vaccines. In general, althoughshort-cut methods which presuppose some features of the sequence arealso available, the method, in principle, offers the opportunity tomaximize the desired property without preconceived ideas as to the mostsuccessful sequence.

EXAMPLES

The following examples are intended to illustrate but not to limit theinvention.

Example 1 Determination of Coupling Constants

Individual resins in polypropylene bags derivatized to each of the 20DNA-encoded amino acids were prepared and collectively reacted with anequimolar mixture of BOC-protected amino acids in the presence of thecoupling reactant diisopropylcarbodiimide (DIPCDI). The 20 bags, eachcontaining a mixture of resulting dipeptides, were individually treatedto decouple the dipeptides from the resins and the amino acidcomposition of each mixture was determined. The results, discussedbelow, produced relative values of rate constants for most of the 400possible couplings.

In more detail, the synthesis was performed using a modified method ofthat disclosed by Houghten, R. A. (Proc Natl Acad Sci USA (1985)32:5132-5135).

Twenty labeled polypropylene bags (75 u; 1 in. ×1 in.; McMaster-Carr,Los Angeles, Calif.) each containing .sup.˜ 100 mg of p-methyl-BHA-resinhydrochloride (.sup.˜ 0.75 mmol/g; d150-200 mesh; ABI) were gathered ina 250 ml polyethylene wide-mouth screw-cap vessel, washed with 2×100 mlof DCM, and neutralized with 3×100 ml of 5:95 (V/V) DIEA in DCM andwashed with 2×100 ml DCM.

Each bag was labeled with black India ink for identification and placedin separate vessels (125 ml screw cap, Nalgene). To each was added 0.8mmol (10-fold excess) of an amino acid dissolved in 2 ml DCM(A,D,C,E,G,I,K,M.F.P,S,T,Y,V), 0.2 ml DMF and 1.8 ml DCM (R,H,L,W), or 2ml DMF(Q,N), 2 ml of 0.4 mol DIPCDI in DCM (0.8 mmol) was added to eachand 0.8 mmol HOBT was added to the reactions containing Q and N. Thecoupling time was one 1 hour at room temperature with mechanicalshaking. The bags were combined in a 250 ml vessel, washed with 100 mlDMF and then 100 ml DCM. The BOC protecting group was removed bytreatment with 100 ml 55% trifluoroacetic acid in DCM for 30 min. on ashaker.

The gathered bags were washed with 1×100 ml DMF, 2×100 ml of 5% DIEA inDCM and washed with 2×100 ml DCM. The following mixture was added to thecollection of bags: all 20 BOC amino acids (0.8 mmol each), 4.8 ml DMF,and 35.2 ml DCM; 40 ml of a 0.4 molar solution of coupling reactantDIPCD (16 mmol total) in DCM was then added. The AAs were coupled onehour with shaking. The combined bags were washed with 1×100 ml DMF and1×100 ml DCM, and the His DNP-blocking group was removed with 99 mlDMF+1 ml thiophenol; this procedure was repeated. The bags were washedsequentially with 100 ml DMF, 100 ml isopropyl alcohol, and 100 ml DCM,six times.

The bags were placed with 0.5% anisole into separate tubes of a multipleHF apparatus and 5 ml HF was condensed in each tube. The tubes were keptat 0° C. for one hour, the HF was removed with nitrogen gas, and thepeptide-resins were dried in a desiccator overnight. The individual bagswere washed with 2×5 ml ether to remove anisol, dried, and extractedwith 2×5 ml of 15% acetic acid. The extracted dipeptides werelyophilized. A portion of each resin (about 2 mg) was hydrolyzed ingas-phase HCl at 108° for 24 hr and he amino acid composition of eachdipeptide mix was determined by the Pico-tag method.

Table 2 given in FIG. 1 shows the results of amino acid (AA) analysis(AAA) of these bags. The AA bound to resin in the bags are shown acrossthe top. The columns show the amounts in nmole of activated AA attached.The amount of coupling (activated) amino acids was in excess, so theamount of each attached to the resin reflects the relative rateconstants. Several determinations gave reproducible results.

FIG. 2 shows the data of Table 2 normalized to Phe as an activated AA bydividing the amino acid composition of each dipeptide resin by theamount of Phe coupled to that resin; this then shows the relativereactivities of 18 activated amino acids for 20 amino acid resins. Thedata are plotted with the fastest reacting activated AA to the left(i.e., Gly). If each amino acid has the same collection of relativerates of attachment to all resins, the heights of the columns withineach of the 16 clusters (Asn+Asp and Glu+Gln are single clusters) wouldbe constant. (The cluster for Phe is of course flat, as it is used as abase for normalization.) The results show that, in fact, within acluster, the heights generally vary no more than about 20%.

The relative heights of the different clusters reflect the relativereactivities of the various activated amino acids. The average of eachcluster thus gives a good (inverse) approximation of the amount ofactivated AA to be used in coupling mixture AAs to all AA-resins.

Results of the foregoing amino acid analysis are subject to thefollowing reservations: First, Trp and Cys are destroyed in the analysisand thus do not appear with values in the results; these could befurther analyzed if necessary. Second, the amides in Gln and Asn arehydrolyzed in the analysis so that the values presented for Glu and Asprepresent Glu+Gln and Asp+Asn, respectively. Third, since the amino acidattached to the resin is present in such large amount--i.e., 50% of thetotal--the small amount of the same amino acid coupled to it cannot beassessed in a particular experiment; however, the approximate amount canbe surmised from the other data points.

EXAMPLE 2 Synthesis of Dipeptide Mixtures

The use of the determined rate constants in preparing dipeptide mixturesis illustrated here. Five different AA-resins were reacted with amixture of 4 activated AAs. The concentrations of the activated AAs wereadjusted using rate constants from Example 1 to give near eguimolarproducts. The synthesis was performed by the T-bag method of Example 1and automated synthesizer.

Five 74 micron 1×2 inch polypropylene bags were prepared. The bags werelabeled for identity with black india ink, and filled with .sup.˜ 100 mgof p-methyl-BHA-resin hydrochloride (.sup.˜ 0.75 mmol/g, 150-200 mesh).They were combined in a Nalgene bottle (125 ml) and washed 2×25 ml DCM.(All washing and coupling procedures were performed on a mechanicalshaker.) The resin was neutralized in the same bottle with 3×25 ml of 5%DIEA in DCM (2 min each) and then washed with 2×25 ml of DeM. The resinswere reacted in separate vessels (30 ml Nalgene bottle) with 0.8 mmol(.sup.˜ 10-fold excess) of one of the following amino acids (tBOC-Glu,tBOC-Ile, tBOC-Met, tBOC-Ala, tBOC-Gly) dissolved in 2 ml DCM, using 0.8mmol (2 ml of a 0.4 M solution) of DIPCDI in DCM as a coupling reagent.The coupling time was one hour at room temperature. The bags werecombined in a 125 ml Nalgene bottle and washed with 25 ml DMF and then25 ml DCM. For the coupling the ABI 430/A synthesizer and reagentssupplied by the manufacturer were used (except 50% TFA in DCM was usedinstead of neat TFA), along with a program provided by C. Miles. Thefive bags containing the different amino acids on the resin (.sup.˜0.4-0.5 mmol) were placed into the standard reaction vessel so the resinis towards the bottom. The mixture of activated AA was supplied as acartridge containing 108 mg (0.467 mmol) tBOC-Leu, 77 mg (0.292 mmol)tBOC-Phe, 198 mg (0.914 mmol) tBOC-Val, 72 mg (0.336 mmol) tBOC-Pro. Thetotal of all amino acids was 2.09 mmol. The ABI Phe program was used forcoupling. About 5 mg peptide was removed for peptide resin sequencingand a portion was hydrolyzed for amino acid analysis using concHCl-propionic acid (1:1) as described by Scotchlet, J., J. Org. Chem.(1970) 35:3151.

The results are shown in FIG. 3. This shows that the relative rate foreach activated AA is quite similar with respect to all resins, and thatthe resulting mixture is nearly equimolar. A perfect result would givethe value 0.25 for each product and equal heights within each cluster.The actual result has a range of 0.20-0.32 and the average is 0.25±0.04(SD). Overall, each amino acid is no more than 0.8 to 1.28 times thedesired amount.

Example 3 Synthesis of Defined Mixtures with Constant Positions

The method of the invention wherein mixtures of amino acid residuesalternate with blocks of known constant composition is illustrated inthis example. The approach is also applicable to synthesis of mixturesin general.

The peptides Gly₁ -AA₂ -Ala₃ -AA₄ -Gly₅ are synthesized wherein AA₂ isselected from Lys, Met, Set, and Tyr, and AA₄ is selected from Leu, Pro,Phe, and Val. The mixture has, therefore, 16 possible peptides. If therate constants for all possible couplings are known, the productcomposition can be calculated from the coupling constants and therelative concentrations of the activated amino acids added at each step.Conversely, if the desired product ratio is known, the requiredconcentrations can be derived by a suitable algorithm. Two separatesyntheses were conducted, one using equimolar amounts of reactants, andthe other using amounts adjusted to form an equimolar mixture of theresulting peptides.

In the first synthesis, conducted on an ABI 430 synthesizer usingprograms and reagents supplied by the manufacturer, tBOC-Gly-PAM resinwas deblocked and coupled to a mixture containing equimolar amounts ofthe four tBOC amino acids Val, Phe, Leu, and Pro. The resulting bounddipeptides were then coupled to tBOC-Ala, followed by coupling to anequimolar mixture of tBOC-protected Lys, Met, Set and Tyr. Finally,tBOC-Gly was used to provide the fifth residue. The peptide was cleavedfrom the resin and analyzed to obtain the pertinent rate constant data.

In the second synthesis, the rate constants obtained above were used tocalculate the concentration of each amino acid necessary to produce apeptide mixture having equal molar amounts of each peptide product. Thesynthesis was performed as above, but with the adjusted concentrations.

First Synthesis, Eguimolar Reactants

In more detail, 0.62 g (0.5 mmol) tBOC-Gly-PAM resin was obtained in thefirst cycle. In the second cycle, a mixture (2.0 mmol total) containing0.5 mmol each of tBOC-Val (0.108 g), tBOC-Phe (0.132 g), tBOC-Leu (0.126g), and tBOC-Pro (0.107 g) was coupled to the supported Gly using theABI Phe program. In the third cycle, 0.378 g (2.0 mmol) tBOC-Ala wasreacted. In the fourth cycle, a mixture (2.0 mmol total) containing 0.5mmol each of tBOC-Lys(Cl-Z) (0.207g), tBOC-Met (0.124 g), tBOC-Ser(OBzl)0.147 g) and tBOC-Tyr(OBzl) (0.185 g), was coupled using the Lysprogram. In the fifth cycle, the coupled amino acid was 0.352 g (2.0mmol) tBOC-Gly.

After each coupling, the resin was analyzed for unreacted free amine andcoupling was over 99.7% complete.

The synthesis was interrupted after coupling of the first amino acidmixture and a small sample (ca. 10 mg) was analyzed by sequencing theresin-peptide (ABI User Bulletin No. 4, 1985). The amino acids in [AA₂ ]were not analyzed because of their side-protecting groups. The weight ofthe peptide-resin at the end of the synthesis was 0.787 g; theoreticalis 0.804 g to 0.912 g.

The mixture of peptides was cleaved from the resin using 7 ml condensedHF and 0.7 g p-cresol as scavenger during 1 h at 0°. The HF was removedby a stream of N₂ and the excess of p-cresol was removed by extractionwith 2×10 ml ethylacetate. The peptides were extracted with 15% aceticacid, lyophilized, dissolved in 5 ml water, and lyophilized again; somematerial was lost during lyophilization. A white solid was obtained(0.150 g) (theoretical, 0.20g), and was analyzed as described below.

HPLC system: A solution of 100 μl of crude peptide in 10 μl 0.1%TFA/water was loaded on Vydac C18 column (4.6 mm×25 cm). Solvent A was0.1% TFA in water; solvent B was 0.1% TFA in acrylonitrile (ACN); thestandard gradient was 0-55% B in 55 min at a flow rate 1.00 ml per min;the flattened gradient was 0.35% B over 120 min. Detection was at205-300 nm using a Hewlett-Packard Diode Array Detector (DAD).

Sequencing: For sequencing the pentapeptides attached to resin, 5-10 mgpeptide resin was suspended in 100 μl 25% TFA and 5.1 was loaded to ABI430A gas-phase sequencer using 03RREZ program. For the free peptides,200 μg of the peptide mixture was dissolved in 1 ml water and 1 μl (400pm) was loaded to the sequencer (03RPTH program). An on-line PTHanalyzer (ABI 120 A HPLC) was used, loading about 25 pm of PTH-AAstandards. Quantitation was by computer-assisted integration.

FIG. 4A shows a single-wavelength HPLC chromatogram of the pentapeptidemixture Gly-[Lys,Met, Ser,Tyr]-Ala-[Leu,Pro,Phe,Val]-Gly from theinitial systhesis. In this determination, 15 of the 16 expected peptideswere identified; each of these 15 peptides contained the appropriate AAsin the expected stoichiometry. Peak 2a/2b shown in FIG. 4A, contains twosequences: Gly-Ser-Ala-Val-Gly and Gly-Lys-Ala-Leu-Gly. The former isone of the expected peptides, but the latter is identical to the peptidein peak 3. Since 18 is probably a highly hydrophobic peptide (by RV), wesuspect it may still contain the Lys-blocking group (C1-Z). Also, peak15 contains two peptides, Gly-Phe-Ala-Met-Gly and Gly-Phe-Ala-Tyr-Gly.This conclusion was confirmed by mixture sequencing of the purifiedpeak. These two peptides were later separated on HPLC by lowering thesteepness of the gradient to 0-35%B, 120 min.; the peak areas werenearly identical (10700 vs 10794, respectively).

Only one of the expected 16 peptides was not identified in this HPLCanalysis. Since all peptides are evident by sequence analysis, wepresume this peptide was present but undetected. Two sets of peaks (4and 13; 9 and 15a) seem to contain the same AAs and thus have the samesequence; the faster moving minor peaks in each set were assigned as theMet-sulfoxide, formed during workup. Peaks 16, 17, and 19 are eachmissing one of the mixed amino acids (they appear as tetrapeptides) andcannot be assigned from these data.

FIG. 4B shows the same mixture using the multi-wavelength detection of aHewlett-Packard Diode Array Detector (DAD). The results shown in FIG. 4Bprovide complete spectra for each of the peaks; notably, the aromaticside chains can be seen above 240 nm and peptides containing Trp,Tyr,Phecan be readily identified.

FIG. 5 shows estimates of the amounts of each aromatic amino acid ineach peptide, using ratios of integrated absorbances at 215,254 and 280nm and second derivative analysis (which, for example, rules out Trp inthese cases). FIG. 5 shows a plot of the HPLC peaks of FIG. 4A vs.number of aromatic AAs (no peptides have Trp; 3 peptides (8, 10, 15a)have 1 Phe only; 3 peptides (6, 11, 13) have 1Tyr only; 1 peptide (15b)has 1 Tyr and 1 Phe).

A sample of each peak from a parallel run (not shown) of the same samplewas subjected to AAA; in this run peaks 13 and 14 were separated, but15a and 15b merged into peak 15, and the peaks labeled 2a/2b and 2c inFIG. 4A merged as well into a single broad peak, peak 2. An earlyfraction, a late fraction, and a pooled fraction of peak 2 wereseparately analyzed; peak 15 was separated on another HPLC run byreducing the gradient to 0-35%B, 120 min, and the separated peaks werecollected for AAA. Table 3, shown in FIG. 6 shows these results.

From these data 15 of the 16 expected peptides were clearly identified.The remaining one of the predicted 16 peptides (Gly-Lys-Ala-Val-Gly) wasdeduced to be in the pool of peak 2, as evidenced by the mixed AAanalysis; it is masked by the two known peptides (Gly-Lys-Ala-Pro-Glyand Gly-Ser-Ala-Val-Gly) in the peak. Each of the 15 peptides identifiedcontains the appropriate AAs in the expected stoichiometry. Two smallpeaks (4 and 12) seem to contain the same AAs and thus have the samesequence as two of the major peaks (13 and 15a, respectively); thefaster moving minor peak in each set was assigned as the Met-sulfoxide,formed during workup.

Table 4 (FIG. 7) gives the results of sequencing the peptide-resin andthe HF-cleaved peptide mixture. From sequencing the peptide-resin, themixture of four AAs in position 2 were not identified because of theblocking group on the AAs. After HF cleavage, which provides theunblocked peptide, each of the AAs in positions 2 and 4 were identifiedand quantitated. Some loss of free peptide from the filter occurred witheach cycle, but the relative amounts of AA in each cycle should beaccurate. In both sequencing experiments the intervening Ala cycle wasclean (i.e., no other AAs were observed).

Table 4 also gives analyses of the mixture of peptides. The normalizedamounts are in good agreement with the values obtained by sequencing.The Val may be slightly underestimated by sequencing of free orresin-bound peptide since the higher AAA value probably provides a moreaccurate value. The Pro may be overestimated in sequencing of the freepeptide, and Tyr may be slightly underestimated (due to partdestruction) in AAA.

AA₄ defines the mole fractions of each of four sets of peptides and eachof these sets contains four peptides defined by the AAs in AA₂. Becauseof the expansion in numbers of peptides at coupling of AA₂, theambiguities do not permit direct quantitation of individual sequences.For the sequence assignment in Table 4 it was assumed that coupling ofany AA at AA₂ is independent of the variable AA at position 4. In thismanner, the amount of each of the peptides (mole fraction AA₂ ×molefraction AA4=mole fraction peptide) was calculated. Estimating thecomposition of the pentapeptide mixture using data from sequencing thefree peptides, and from AAA (Table 3), the compositions deduced (Table4) are in fairly good agreement.

Using the composition of the peptides in the mixture produced above, asto the relative amounts of variable AAs, as determined by sequencing thefree peptides and the amount of reactants used, the rate constant foreach coupling was calculated (Table 4, FIG. 7). The resulting relativerates are in reasonable agreement with those of the Kemp and Kovacsvalues for coupling to Gly, except for Val, which here reacts faster.This discrepancy is attributed to different methods of coupling, i.e.,p-nitrophenyl vs symmetrical anhydride. The conclusion that the rateconstant for coupling of Val is indeed different is supported by theresults of the reaction of a mixture of these amino acids (and others)with Gly-resin as described elsewhere in the "20×20 experiment" and alsoshown in this table.

Adjusted Reactants

Based on the rate constants obtained above, a second synthesis wasdesigned and performed using an analogous method. To 0.5 mmol Gly-PAMresin was coupled 0.12 g (0.48 mmol) tBOC-Leu, 0.08 g (0.308 mmol)tBOC-Phe, 0.21 g (0.95 mmol) tBOC-Val, and 0.06 g (0.26 mmol) tBOC-Pro.After coupling 0.39 gm tBOC-Ala (2 mmol), a mixture of four amino acidswere coupled: 0.26 g (0.64 mmol) tBOC-Lys(C1-Z), 0.13 g (0.53 mmol)tBOC-Met, 0.17 g (0.46 mmol) tBOC-Tyr(OBzl), and 0.11 g (0.37 mmol)tBOC-Ser(OBzl). Finally, the N-terminal tBOC-Gly (0.35 g; 2 mmol) wascoupled. The mixture was processed as described for the above synthesis,some material was lost during lyophilization. The weight of the mixedpeptides was 120 mg.

The reaction amounts were designed to produce peptide mixture withequimolar amounts of each peptide (i.e., 25% of peptide has eachcandidate amino acid in each mixture position). The synthesis wasperformed with 99.78% to 99.83% coupling efficiency. Analysis of thepeptide mixture was performed, as above, by sequencing free andresin-bound peptide, as well as amino acid analysis. As before, Peak 13was large and suspected to consist of two peptides. It wasrechromatographed using the flattened gradient to resolve two peaks. TheAAA of the two peaks were in accord with the structures (Peak 13:Gly-0.71, Ala-0.34, Met-0.32, Phe-0.33; peak 14: Gly-0.55, Ala-0.26,Tyr-0.24, Phe-0.25). With the exception of Pro, which appears low onresin-peptide sequencing, agreement among the methods is excellent. Theanalysis indicates that the component AAs at each of the two mixturesites are present in nearly the same ratio (0.25=0.05 S.D.),significantly more similar than the first experiment. The average of allanalyses was used for these calculations. If the sequencing results ofthe free peptides are used (the method used to determine the k values),the error is slightly less at 0.25±0.04; the range is 0.2 to 0.31.

It was thought that the low Pro in this experiment might be due to anerroneous relative rate constant derived from sequencing of the freepeptide (Table 4, above); as noted, both AAA and sequencing of thepeptide resin in the first experiment gave lower Pro values and, ifthese were used, would have prompted the use of more Pro to achieveequimolar peptides. Several mixed dipeptides (AA₄ -AA-resin) were thusmade using relative rate constants obtained from the peptide-resinsequence quantitation in Table 4; also, the ABI synthesizer was used tocouple the mix to 4 AA-resins contained in the reaction vessel. AAA ofthe peptides showed coupling of a mixture of Leu, Phe, Pro, Val toGly-resin proceeded as predicted with SD/Mean=0.15. Further, coupling ofthe mix to resins (Ala, Glu, Ile, and Met) went as expected, withvariations SD/Mean .sup.˜ 0.15. As predicted, the relative rate constantused for Pro in the initial coupling was an erroneous one; a lower valueshould henceforth be used.

Example 4 Synthesis of Di-, Tri-, Tetra- and Pentapeptides

This examples describes the synthesis of balanced mixtures of the3,200,000 possible pentapeptides, 160,000 tetrapeptides, 8000tripeptides, and 400 dipeptides, in a manner similar to the synthesis ofmixed peptides described in Examples 1-3 except that the AA-resins arenot separated.

An equimolar mixture of the 20 AA-PAM-resins is prepared; the mixture isreacted to completion with a mix of C-20 activated N-blocked aminoacids. A portion of the dipeptide mixture is removed and deblocked; thereaction is repeated with an identical mix of amino acids, and the cycleis repeated several times. The amounts of amino acids used are based onrelative rate determinations, and adjusted to approximate first-orderkinetics by having each amino acid in at least 10-fold excess over itsfinal product. Relative rates are determined by averaging from valuesgiven in FIG. 1 and additional data.

The 20 tBoc-AA-PAM resins (ABI) were combined to give an equimolarmixture of 1 mmol of total resin-linked, protected (9 of 20), tBoc-AA.The resin mixture was swollen in 2×50 ml DCM, and filtered. The tBocprotecting group was removed and the resin neutralized as describedpreviously.

A mixture of 20 tBoc-amino acids was prepared by dissolving thefollowing (total of 20 mmol) in 6.0 ml DMF/44 ml DCM:

Gly, 84 mg=480 umol;

Ala, 113 mg=599 umol;

Arg (Tos), 286 mg=666 umol;

Phe, 177 mg=668 umol;

Glu(OBzl), 230 mg=682 umol;

Gln, 168 mg=682 umol;

Met, 176 mg=705 umol;

Pro, 157 mg=730 umol;

Asp(OBzl), 238 mg=737 umol;

Asn, 171 mg=737 umol;

Leu, 185 mg=801 umol;

Ser(Bzl), 243 mg=825 umol;

Lys(Cl-Z), 387 mg=933 umol;

Tyr(Br-Z), 485 mg=981 umol;

Thr(Bzl), 451 mg=1459 umol;

His(DNP), 668 mg=1585 umol;

Val, 510 mg=2349 umol;

Ile, 667 mg=2889 umol;

Cys(4-me-Bzl), 268 mg=825 umol;

Trp, 203 mg=668 umol.

The amino acid mixture was combined with the resin mixture; 30 ml of a0.67 molar solution of coupling reactant DIPCD (20 mmol total) in DCMwas then added and the AAs were coupled one hour with shaking. The resinwas washed with 2×80 ml DMF and 2×80 ml DCM. An aliquot (50 umolpeptide-resin) was removed, dried, weighed and saved for subsequenttreatment with DMF+i ml thiophenol (DNP-His deblocking) and HF cleavageas before to give the mixture of 400 dipeptides.

This process was repeated on the remaining resin 3 more times, to givethe mixed tri-, tetra- and pentapeptides.

Example 5 Selection for Binding to Papain

N-acetyl phenylalanyl glycinaldehyde is a potent inhibitor of papain;the Phe group binds to the P2 site of papain and the aldehyde binds theactive site thiol in a reversible covalent bond. A mixture of variousN-acetyl aminoacyl glycinaldehydes was treated with papain and thecomponents capable of binding to papain were selected.

Papain (15 uM) and DTT (10 mM), potassium phosphate (20 mM)-EDTA (1 mM),pH 6.8 (P-E buffer) and a mixture of the N-acteylaminoacylglycinaldehydes of Phe Gly, Ala, Val, Leu, Ile, Met, Pro, Asnand Gln (25 uM each, 250 uM total inhibitor) were added. Total volumewas 300 ul; concentrations given are for the final mixture. After 10min. at room temp., 150 ul was applied to a Sephadex G-10 column (1cm×4.2 cm, 3 ml column volume) at 4° C. The column was equilibrated andeluted in P-E buffer at 0.45 ml/min.

The fractions corresponding to the void volume were collected andtreated with 14 mM thiosemicarbazide in 0.1M HCl to convert thealdehydes to thiosemicarbazones. The products were analyzed on a VydacC18 column eluted with an 0 to 60% water/acetonitrile gradient usingdiode array detection.

The main fraction contained a predominance of the Phe analog derivative(0.7 uM phe/3 uM; initially present as the N-acetyl phenylalanylglycinaldehyde-papain complex) which is at least 10-fold enriched overthe other analogs.

We claim:
 1. A method of obtaining a peptide having a desired targetproperty, comprising the steps of:providing a mixture of candidatepeptides containing 8,000 or more different peptides of distinct, uniqueand different amino acid sequences, wherein the presence of each peptidein the mixture is predetermined, each peptide is present in the mixturein retrievable and analyzable amounts and the mixture includes at leastone biologically active peptide in a retrievable and analyzable amount;and selecting from among the mixture of candidate peptides a peptidehaving a desired target property by exposing the mixture of candidatepeptides to a substance to which the peptide having a desired targetproperty will preferentially bind.
 2. The method as claimed in claim 1,further comprising:isolating the selected candidate peptide having thedesired target property.
 3. The method as claimed in claim 2, furthercomprising:identifying the isolated candidate peptide having the desiredtarget property.
 4. The method as claimed in claim 1, wherein themixture of candidate peptides contains 160,000 or more differentpeptides of distinct, unique and different amino acid sequences, each inretrievable and analyzable amounts, and wherein the presence of eachpeptide in the mixture is predetermined.
 5. The method as claimed inclaim 1, wherein the mixture of candidate peptides contains 3,200,000 ormore different peptides of distinct, unique and different amino acidsequences, each in retrievable and analyzable amounts, and wherein thepresence of each peptide in the mixture is predetermined.
 6. The methodas claimed in claim 1, wherein the mixture of candidate peptidescontains 64,000,000 or more different peptides of distinct, unique anddifferent amino acid sequences, each in retrievable and analyzableamounts, and wherein the presence of each peptide in the mixture ispredetermined.
 7. A method of obtaining a peptide having a desiredtarget property, comprising the steps of:providing a mixture ofcandidate peptides containing 8,000 or more different peptides ofdistinct, unique and different amino acid sequences, wherein thepresence of each peptide in the mixture is predetermined and eachpeptide is present in an amount such that each peptide is analyzable;and selecting from among the mixture of candidate peptides a peptidehaving a desired target property by exposing the mixture of candidatepeptides to a substance to which the peptide having a desired targetproperty will preferentially bind.
 8. The method as claimed in claim 7,further comprising:isolating the selected candidate peptide having thedesired target property.
 9. The method as claimed in claim 8, furthercomprising:identifying the isolated candidate peptide having the desiredtarget property.
 10. The method as claimed in claim 7, wherein themixture of candidate peptides contains 160,000 or more differentpeptides.
 11. The method as claimed in claim 7, wherein the mixture ofcandidate peptides contains 3,200,000 or more different peptides. 12.The method as claimed in claim 7, wherein the mixture of candidatepeptides contains 64,000,000 or more different peptides.
 13. A method ofobtaining a peptide having a desired target property comprising:a)synthesizing a mixture of peptides by reacting a predetermined amount ofan activated amino acid residue with an acceptor amino acid or peptidein a manner so as to obtain a mixture of peptides containing 8,000 ormore different peptides of distinct, unique and different amino acidsequences wherein the presence of each peptide in the mixture ispredetermined, each peptide is present in the mixture in retrievable andanalyzable amounts; and b) selecting peptides having one or more desiredtarget properties by exposing the mixture of peptides to a substance towhich the peptides having one or more desired target properties willpreferentially bind.
 14. The method of claim 13 wherein the peptidemixture contains 160,000 or more peptides in known quantities.
 15. Themethod of claim 14 wherein the peptide mixture contains 3,200,000 ormore peptides in known quantities.
 16. The method of claim 15 whereinthe peptide mixture contains 64,000,000 or more peptides in knownquantities.
 17. A method of obtaining a peptide having a desired targetproperty comprising:a) combining and reacting activated amino acids withan acceptor amino acid or peptide, wherein the concentration ofactivated amino acid added is varied depending on its coupling constantso as to obtain a candidate mixture of peptides wherein each peptide ofthe candidate mixture is present in a predicted and analyzable amount;b) selecting peptides having one or more desired target properties byexposing the candidate mixture to a substance to which the peptidehaving one or more desired target properties will bind; and c) isolatingpeptides which selectively bind to the substance from the candidatemixture.
 18. The method of claim 17, wherein selecting step b) isfurther comprised of a second selection step, such that the resultingselected peptides exhibit a greater degree of the desired targetproperty.
 19. A method of obtaining a peptide ligand from a candidatemixture of peptides, said peptide ligand being a ligand of a giventarget molecule, comprising:a) combining and reacting activated aminoacids with an acceptor amino acid or peptide, wherein the concentrationof activated amino acid added is varied depending on its couplingconstant, such that each peptide of the candidate mixture is present ina predicted and analyzable amount; and b) isolating peptides having anincreased affinity to the target molecule by exposing the candidatemixture to a substance to which peptides having an increased affinity tothe target molecule will preferentially bind.